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| Status |
Public on Nov 08, 2021 |
| Title |
Investigating Immune and Non-Immune Cell Interactions in Head and Neck Tumors by Single-Cell RNA Sequencing |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Head and neck squamous cell carcinoma (HNSCC) is characterized by complex relations between stromal, epithelial, and immune cells within the tumor microenvironment (TME). To enable the development of more efficacious therapies, we aim to study the heterogeneity, signatures of unique cell populations, and cell-cell interactions of suppressive non-immune and immune cell populations in 6 human papillomavirus (HPV)+ and 12 HPV- HNSCC patient tumor and matched peripheral blood specimens using single-cell RNA sequencing (scRNAseq). Using this dataset of 134,606 cells, we show cell type-specific signatures associated with inflammation and HPV status, describe the negative prognostic value of fibroblasts with elastic differentiation specifically in the HPV+ TME, predict therapeutically targetable checkpoint receptor-ligand interactions, and show that tumor-associated macrophages are dominant contributors of PD-L1 and other immune checkpoint ligands in the TME. We present a comprehensive single-cell view of cell-intrinsic mechanisms and cell-cell communication shaping the HNSCC microenvironment.
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| Overall design |
PBL, CD45+ and CD45- samples from 18 treatment naïve patients were analyzed in this study
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| Contributor(s) |
Ferris RL, Kulkarni A, Kurten C, Vujanovic L |
| Citation(s) |
34921143, 35392082 |
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| Submission date |
Jan 12, 2021 |
| Last update date |
Apr 19, 2022 |
| Contact name |
Robert L Ferris |
| E-mail(s) |
ferrisrl@upmc.edu
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| Organization name |
University of Pittsburgh
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| Street address |
5500 Center Ave
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| City |
Pittsburgh |
| ZIP/Postal code |
15232 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (51)
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| Relations |
| BioProject |
PRJNA691564 |
| SRA |
SRP301444 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE164690_RAW.tar |
718.2 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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